Trace metals like copper (Cu) and zinc (Zn), essential at low concentrations but toxic in excess, contrast with non-essential metals like cadmium (Cd) and lead (Pb), significant environmental contaminants. Conventional and organic agriculture employ varying agrichemical inputs, including trace metals. Elevated trace metals in aquatic environments can harm waterbirds, with oxidative metabolism changes indicating environmental stress. We compared trace metal concentrations (Pb, Zn, Cd, Cu) in feathers and biomarkers in muscle and liver tissue of waterbirds from organic and conventional irrigated rice farms in South Brazil. Biomarkers included catalase (CAT) and superoxide dismutase (SOD) activity, protein carbonylation (PC), lipid peroxidation (LPO), and non-protein thiols (NPSH) concentration. Cu and Pb concentrations were higher in waterbirds from conventional farms, whereas Cd and Zn levels were elevated in organic farms. Birds foraging in organic farms exhibited lower CAT and SOD activity and higher NPSH, LPO, and PC concentrations compared to those in conventional farms. Higher Cu and Pb concentrations were associated with elevated SOD and CAT activity, more prevalent in birds frequenting conventional farms. Conversely, birds with higher Cd and Zn concentrations showed increased NPSH, LPO, and PC levels and were more common in organic farms. Our study underscores complex differences in trace metal accumulation and oxidative stress biomarkers among waterbirds in organic and conventional rice crops.